The DADA2 removeBimeraDenovo() function fails to detect some perfect chimeras. An example is given below of a perfect chimera (i.e., an exact match to two segments from sequences with higher abundance) that is not found by DADA2 v.0.99.10. Above is the alignment generated by uchime2_denovo and below are the sequences.
>sq1;size=533608;
GGCGGCGTGCCTAATACATGCAAGTCGAGCGAGTCTGCCTTGAAGATCGGAGTGCTTGCACTCTGTGAAACAAGATACAG
GCTAGCGGCGGACGGGTGAGTAACACGTGGGTAACCTGCCCAAGAGATCGGGATAACACCTGGAAACAGATGCTAATACC
GGATAACAACAGATGATGCCTATCAACTGTTTAAAAGATGGTTCTGCTATCACTCTTGGATGGACCTGCGGTGCATTAGC
TAGTTGGTAGGGTAACGGCCTACCAAGGCGATGATGCATAGCCGAGTTGAGAGACTGATCGGCCACATTGGGACTGA
>sq233;size=82;
GGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTGCTTGCAGGGTGCTCGAGTGGCGAACGGGTGAGTAACAC
GTGGGTGATCTGCCCCTTACTTTGGGATAAGCCTGGGAAACTGGGTCTAATACTGGATAGGACCATGCTGTAGGTGGTGT
GGTGGAAAGATTAGTTTCGGTAAGGGATGAGCTCGCGGCCTATCAGCTTGTTGGTGGGGTAATGGCCTACCAAGGCGTCG
ACGGGTAGCCGGCCTGAGAGGGTGGACGGCCACATTGGGACTGAGA
>sq441;size=12;
GGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCTCTGCTTGCAGGGGTGCTCGAGTGGCGAACGGGTGAGTAAC
ACGTGGGTAACCTGCCCAAGAGATCGGGATAACACCTGGAAACAGATGCTAATACCGGATAACAACAGATGATGCCTATC
AACTGTTTAAAAGATGGTTCTGCTATCACTCTTGGATGGACCTGCGGTGCATTAGCTAGTTGGTAGGGTAACGGCCTACC
AAGGCGATGATGCATAGCCGAGTTGAGAGACTGATCGGCCACATTGGGACTGA